As the young billionaire rulers of Saudi Arabia and Qatar attempt to assert their geopolitical dominance, one of the best-known brands in the Middle East, Al-Jazeera, is in the firing line.

Al-Jazeera has been a constant thorn in the side of its neighbors. The news network was the first independent media network in the Middle East, winning plaudits with more than 20 years of broadcasting. But after the Arab Spring, Doha was forced to tone down coverage to maintain stability in neighboring countries, especially in Bahrain.

Qatar has been forging an independent foreign policy since the discovery of gas and a palace coup where the former emir ousted his pro-Saudi leaning father. Since 1995, the country has been on a tear with a construction boom reshaping the desert state. While Qataris are the world's richest per capita ($130,000), more than 35 percent live under the national poverty line in neighboring Saudi Arabia.

"The State of Qatar recognizes that a decision to close Al-Jazeera will infringe on their sovereignty," Wadah Khanfar, the former director general of Al-Jazeera, told CNBC in a phone interview. "The independence of the state is at risk. If they move against Al-Jazeera what next? They will stand firm."

The 3-week-old blockade has seen the closure of borders, airspace and a shortage of some produce in supermarkets, although Iran and Turkey have airlifted various basic goods into the country. Saudi Arabia and other Arab nations have sent Doha a 13-point list of demands, including the closures of Al-Jazeera and Turkey's airbase and the severing of ties with Iran and the Muslim Brotherhood.

In the past, the Arab media was controlled by the state. It was part of the "intelligence structure" but the Saudis and Emiratis still want to control the narrative, Khanfar said. "They see it (Al-Jazeera) as a threat. Al-Jazeera changed the rules of the game."

Khanfar believes that the 31-year-old Saudi Crown Prince Mohammed bin Salman and UAE (United Arab Emirates) Emir Khalifa bin Zayed Al Nahyan have been emboldened by President Donald Trump after his meeting in Riyadh. But he believes they have made a huge miscalculation.

"This debate (to shut down Al-Jazeera) is very old and has been going on since 1996. There is nothing new. But the severity of the blockade is much bigger, much more dramatic," Khanfar said. "Saudis and Emiratis have the impression that Trump is with them. What they fail to see is the president is a transactional leader. That's why they (Saudi Arabia) signed the $110 billion defense deal."

Blockade could backfire

Perhaps more ominously, Turkey – a member of NATO — has fast-tracked the movement of troops to Qatar, and fighter aircraft are to follow. While Saudi Arabia and Bahrain have closed their airspace to Qatari planes, there is a real possibility that Turkey will need to fly over Iran to get to its base in Qatar. That's a point that has not been lost on American officials, according to Qatari government officials, who spoke to CNBC on the condition of anonymity due to the sensitivity of the situation. The Arab coalition has called on Qatar to close down the base.

Iran is already talking to the Turks and the Qataris — a move that could reshape cooperation in the Middle East. And Russian President Vladimir Putin has already spoken to the Qatari Emir and would be eager to mediate, undermining the United States, despite Moscow being accused of hacking the Qatar News Agency website and planting a story that triggered the diplomatic crisis.

Qataris were left "aghast" by Trump's tweet supporting Saudi Arabia and the UAE. His attempts to backtrack and offer to mediate were rejected. His approach is being described as "unreliable and unpresidential," according to Qatari government officials.

Rather than being cowed, the Arabic channel has been hitting back hard at its regional neighbors. "Looks like the gloves are off as coverage has intensified," said one employee, who preferred to remain anonymous.

"My worry is some countries in the region have employed draconian tactics to muzzle any independent media across the Arab world, and Qatar and AJA (Aljazeera Arabic) in this respect is a prime target for their ire. They cannot accept that independent thinkers, reporters, and analysts express their thoughts in public in a manner that is free and independent of official lines," said another.

Job cuts ahead?

In recent days the United Arab Emirates and the Bahrain have warned their citizens not to show sympathy for Qatar, with Abu Dhabi reportedly threatening prison sentences of up to 15 years. Saudi Arabia plans to fine people who watch Al-Jazeera 10,000 Saudi riyals ($2,667), according to the Saudi commission for tourism and national heritage.

"This is shocking. It is not in the culture of the Arab to mete out severe treatment against each other. A lot (of Arabs) are very connected so this kind of treatment is shocking," Khanfar said.

Asked whether employees feared Doha would acquiesce to Riyadh's and Abu Dhabi's demand to shut down the network, many of them pointed to the job losses that had already been undertaken, as oil prices came crashing down. Employees were more concerned the blockade could lead to more economic damage.

"We have been through this (job cuts) and we have survived it. We are more worried about job cuts due to financial crisis than closure, which is a very remote possibility," an employee told CNBC via Facebook messenger.

Qatar isn't averse to sacrificing projects. The network shut down its ambitious plans to take the brand into the United States. After spending billions of dollars on Al-Jazeera America – it's poor viewership was enough for the present emir – 37-year-old Tamim bin Hamad Al Thani.

"This network was the creation of the father emir, and the current emir doesn't think it is such an important asset," said an employee, who also preferred to remain anonymous.

The network has been accused of giving voice to the Muslim Brotherhood, which has been designated a terrorist organization in Saudi Arabia, the United Arab Emirates and Egypt. In the wake of Trump's tweet appearing to back the Saudi cause, employees were quick to reply.

"None of the 9/11 terrorists were from Qatar. Fifteen came from Saudi, two from the UAE and one from Egypt. Qatar is more progressive; women can drive here," said one employee.

But there could be some sacrifices. A team of executives descended on Al-Jazeera's London broadcast center last month and is expected to cut jobs. The network is also likely to get rid of some management executives with direct input into news coverage. These had been long planned but now would be a good time to dust off the plans, according to a person familiar with the decision making at the network.

"I must admit that the Arabic channel has not been very wise or professional in running balanced story coverage. More Arabs now have doubts about its intentions or agenda, but they don't believe their own media either," said one individual familiar with the plan.

Al-Jazeera did not return calls for comment.

CNBC interviewed almost a dozen Qataris, former and present employees of Al-Jazeera for this article.

Abid Aliwas the business and economics editor of Al-Jazeera English between August 2008 and November 2015.